Mitochondrial and nuclear genome interactions are required for efficient mitochondrial function. Polymorphisms in both genomes within natural populations likely contribute to phenotypic variation as different mitochondrial haplotypes and nuclear genomes are combined within individuals. A full understanding of the genetic basis to complex human diseases will require interpreting the contributions of the nuclear genome, the mitochondrial genome, and the role of mitochondrial-nuclear genome interactions. Here, we propose to use a collection of natural isolates of Saccharomyces cerevisiae to characterize mitochondrial-nuclear interactions. Specifically, we will determine the extent to which cellular fitness is affected when different naturally occurring variants of mitochondrial and nuclear genomes are combined. In Aim 1, we will determine if mitochondrial-nuclear epistatic interactions are likely to contribute to coevolutionary processes by testing if the interaction effects follow genetic distance or habitat origin. In Aim 2, we will map the genetic basis underlying mitochondrial-nuclear interactions by identifying nuclear genes contributing to complex traits in these natural isolates. Because of the powerful genetic system available in S. cerevisiae, we will be able to verify the contribution of identified alleles to mitochondrial phenotypes. This research may transform how disease mapping is done in human populations, provide novel insights into uncharacterized genes that are involved with mitochondrial function, and inform future research aimed at elucidating mitochondrially-targeted therapeutic agents for complex human diseases.